Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 90 of 145
Found at i:30847724 original size:14 final size:13
Alignment explanation
Indices: 30847705--30847735 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
30847695 TGGGTACAAG
30847705 TATATATATAAAAA
1 TATATATA-AAAAA
30847719 TATATATAAAAAA
1 TATATATAAAAAA
30847732 TATA
1 TATA
30847736 CGTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TATATATAAAAAA
Found at i:30850138 original size:149 final size:150
Alignment explanation
Indices: 30849705--30850138 Score: 606
Period size: 153 Copynumber: 2.9 Consensus size: 150
30849695 AACATGTTCG
* * *
30849705 TATTTCGG-CCTTTTTTTCGTATTTTTTTCTCGGATTTTATTA-TTTTAAAAAAATATAATATTT
1 TATTTCGGCCCTTTGTTT-GTATTTTTTCCCCGGATTTTATTACTTTT-AAAAAATATAATATTT
* * * *
30849768 TCTAATTT-TCTAATTTTACATTATTTTGGTACATTATATTTGAAATATATTCATTCAGTGTGTT
64 TCTAATTTAT-T-ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTT
30849832 TTTTAAATAAATTAAAAAAACCCT
127 TTTTAAATAAATTAAAAAAACCCT
* * * * *
30849856 TATTTCGACCCTTTGTTTGTATTTTTTCCCTGAATTTTATTACTTTCAATAAAAATATATTATTT
1 TATTTCGGCCCTTTGTTTGTATTTTTTCCCCGGATTTTATTACTTT-TA-AAAAATATAATATTT
* * * * *
30849921 TCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTATGT
64 TC-TAATTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
30849986 TTTAAATAAATTAAAAAAACCCT
128 TTTAAATAAATTAAAAAAACCCT
*
30850009 TATTTCGGCCCTTTGTTTGTA-TTTTTCCCCGGATTTTATTACTTTTAAAAAATATACTATTTTC
1 TATTTCGGCCCTTTGTTTGTATTTTTTCCCCGGATTTTATTACTTTTAAAAAATATAATATTTTC
*
30850073 TAATTTATTATTTTACATTATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTTT
66 TAATTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
30850138 A
131 A
30850139 TTGAAAGTAA
Statistics
Matches: 249, Mismatches: 28, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
149 60 0.24
150 16 0.06
151 28 0.11
152 34 0.14
153 104 0.42
154 6 0.02
155 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (150 bp):
TATTTCGGCCCTTTGTTTGTATTTTTTCCCCGGATTTTATTACTTTTAAAAAATATAATATTTTC
TAATTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
AAATAAATTAAAAAAACCCT
Found at i:30850659 original size:156 final size:155
Alignment explanation
Indices: 30850281--30850722 Score: 617
Period size: 156 Copynumber: 2.8 Consensus size: 155
30850271 NNNNNNNNNN
* *
30850281 TTACATTATTTTAGTACATTATGTTTGAAATGTATAAATTTACTGTG-TTTTTTAAATAAATTTA
1 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAA-TTAGTGTGTTTTTTTAAATAAATTTA
*
30850345 AAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGTATTTTATTAC-TT---TAAAA
65 AAAAAAA-CCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAA
*
30850406 AATATATTACTTTCTAATTTTATTATT
129 AATATATTACTTTCTAATTTTAATATT
* *
30850433 TTACATTATTTTAGTACATTATGTTTGAAATTTATTCATTTAGTGTGTTTTTTTAAATAAATTTA
1 TTACATTATTTTAGTACATTATGTTTGAAATGTATT-AATTAGTGTGTTTTTTTAAATAAATTT-
*
30850498 AAAAAAAACCTTATTTCGGCCCTTTATTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAA
64 AAAAAAAACCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAA
* *
30850563 AATATATTA-TTTTTTATTTTAATATT
129 AATATATTACTTTCTAATTTTAATATT
*
30850589 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAGTGTGTTTTTTTATATAAATTTAG
1 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAGTGTGTTTTTTTAAATAAATTTA-
* * * *
30850654 TAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTTCCGGATTTTATTACTTTCAA
65 AAAAAAAC-CTTATTTCGGCCCTTTGTTCGTA----T-TTTTTTCCCGAATTTTATTACTTTCAA
30850719 TAAA
124 TAAA
30850723 TATACTATTT
Statistics
Matches: 259, Mismatches: 17, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
152 41 0.16
153 61 0.24
154 11 0.04
155 32 0.12
156 70 0.27
157 14 0.05
160 1 0.00
161 29 0.11
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (155 bp):
TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTAGTGTGTTTTTTTAAATAAATTTAA
AAAAAACCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAAA
TATATTACTTTCTAATTTTAATATT
Found at i:30852130 original size:20 final size:20
Alignment explanation
Indices: 30852086--30852124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30852076 AGATTTATCA
* *
30852086 AATTCATATTATTTTATTTC
1 AATTTATATTATATTATTTC
30852106 AATTTATATTATATTATTT
1 AATTTATATTATATTATTT
30852125 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTATATTATATTATTTC
Found at i:30856026 original size:23 final size:23
Alignment explanation
Indices: 30855999--30856044 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
30855989 ATATTTAAAA
**
30855999 TTAAAAAATATAAATTTTATTTT
1 TTAAAAAATATAAAAATTATTTT
*
30856022 TTAAAAAATTTAAAAATTATTTT
1 TTAAAAAATATAAAAATTATTTT
30856045 AAAATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAAAAATATAAAAATTATTTT
Found at i:30861019 original size:27 final size:27
Alignment explanation
Indices: 30860980--30861034 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
30860970 AACTACATGA
30860980 TGTGAGTTGTCTCCACA-AGTGGTGAAG
1 TGTGAGTTGTCTCCACACA-TGGTGAAG
*
30861007 TGTGAGTTTTCTCCACACATGGTGAAG
1 TGTGAGTTGTCTCCACACATGGTGAAG
30861034 T
1 T
30861035 ACGAGATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (27 bp):
TGTGAGTTGTCTCCACACATGGTGAAG
Found at i:30861046 original size:27 final size:27
Alignment explanation
Indices: 30860987--30861109 Score: 88
Period size: 27 Copynumber: 4.6 Consensus size: 27
30860977 TGATGTGAGT
** *
30860987 TGTCTCCACAAGTGGTGAAGTGTGAGT
1 TGTCTCCACAAGTGGTGAAGTACGAGA
*
30861014 TTTCTCCACACA-TGGTGAAGTACGAGA
1 TGTCTCCACA-AGTGGTGAAGTACGAGA
* * * * * *
30861041 TGTCTCTACAACTTGTGAACTATGATA
1 TGTCTCCACAAGTGGTGAAGTACGAGA
* * *
30861068 TGTATCTACAAGTGATG-AGCTACGAGA
1 TGTCTCCACAAGTGGTGAAG-TACGAGA
*
30861095 AGTCTCCACAAGTGG
1 TGTCTCCACAAGTGG
30861110 CAAGTGCAAG
Statistics
Matches: 72, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
26 2 0.03
27 69 0.96
28 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (27 bp):
TGTCTCCACAAGTGGTGAAGTACGAGA
Found at i:30865352 original size:27 final size:27
Alignment explanation
Indices: 30865299--30865370 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
30865289 GGCGAAGTGT
* **
30865299 GAGATGTCTCCAAAAGTGGTAAACTGC
1 GAGATGTCTCCACAAGTGACAAACTGC
* *
30865326 GAGATGTCTCCACAAGTGACGAGCTGC
1 GAGATGTCTCCACAAGTGACAAACTGC
* *
30865353 AAGAAGTCTCCACAAGTG
1 GAGATGTCTCCACAAGTG
30865371 GCAAGTGCGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.19
Consensus pattern (27 bp):
GAGATGTCTCCACAAGTGACAAACTGC
Found at i:30867077 original size:34 final size:35
Alignment explanation
Indices: 30867033--30867099 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
30867023 CAGTAAAATA
*
30867033 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
30867067 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
30867100 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:30876786 original size:18 final size:18
Alignment explanation
Indices: 30876765--30876809 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
30876755 CATTCGTTTC
30876765 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
* *
30876782 ACAAATCGTTATTCAATTT
1 -CAAAACATTATTCAATTT
30876801 CAAAACATT
1 CAAAACATT
30876810 TTTTTTATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Found at i:30885451 original size:3 final size:3
Alignment explanation
Indices: 30885445--30885487 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
30885435 AATAAAAAAA
30885445 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30885488 TTGCCTAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30885711 original size:124 final size:126
Alignment explanation
Indices: 30885478--30885730 Score: 492
Period size: 124 Copynumber: 2.0 Consensus size: 126
30885468 TTATTATTAT
30885478 TATTATTATTTTGCCTAGTACTTGAATTCAATTGAGTGTCTGTTATGTGTTGTGTTTTGTTAGGT
1 TATTATTATTTTGCCTAGTACTTGAATTCAATTGAGTGTCTGTTATGTGTTGTGTTTTGTTAGGT
30885543 AAATGCCTCATAACCCTAATTTGGCGACGGATTTGGATTAAGGGGTGTTACATTTGATTGG
66 AAATGCCTCATAACCCTAATTTGGCGACGGATTTGGATTAAGGGGTGTTACATTTGATTGG
30885604 TATTATTA-TTT-CCTAGTACTTGAATTCAATTGAGTGTCTGTTATGTGTTGTGTTTTGTTAGGT
1 TATTATTATTTTGCCTAGTACTTGAATTCAATTGAGTGTCTGTTATGTGTTGTGTTTTGTTAGGT
30885667 AAATGCCTCATAACCCTAATTTGGCGACGGATTTGGATTAAGGGGTGTTACATTTGATTGG
66 AAATGCCTCATAACCCTAATTTGGCGACGGATTTGGATTAAGGGGTGTTACATTTGATTGG
30885728 TAT
1 TAT
30885731 GAGAGCCACG
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
124 116 0.91
125 3 0.02
126 8 0.06
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (126 bp):
TATTATTATTTTGCCTAGTACTTGAATTCAATTGAGTGTCTGTTATGTGTTGTGTTTTGTTAGGT
AAATGCCTCATAACCCTAATTTGGCGACGGATTTGGATTAAGGGGTGTTACATTTGATTGG
Found at i:30894250 original size:25 final size:26
Alignment explanation
Indices: 30894208--30894268 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
30894198 TTAAGTGTTT
* *
30894208 TCAGTATA-ATCTATCTATAGTAGTC
1 TCAGTATATATCTACCTATAGCAGTC
*
30894233 TCAGTATATA-CTACCTATAGCAGTT
1 TCAGTATATATCTACCTATAGCAGTC
*
30894258 TCAGGATATAT
1 TCAGTATATAT
30894269 TATCAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 29 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (26 bp):
TCAGTATATATCTACCTATAGCAGTC
Found at i:30894608 original size:18 final size:18
Alignment explanation
Indices: 30894585--30894637 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
30894575 AACCGTGTTG
30894585 TTCATTTCCAAAACATTA
1 TTCATTTCCAAAACATTA
* *
30894603 TTCATTTACAAATCATTA
1 TTCATTTCCAAAACATTA
* *
30894621 TACAATTCCAAAACATT
1 TTCATTTCCAAAACATT
30894638 TTTTTATTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (18 bp):
TTCATTTCCAAAACATTA
Found at i:30895372 original size:9 final size:9
Alignment explanation
Indices: 30895358--30895394 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
30895348 TCAGGCTTAA
30895358 TCATATCAG
1 TCATATCAG
30895367 TCATAT-AG
1 TCATATCAG
30895375 TCATA-CAG
1 TCATATCAG
*
30895383 TCATTTCAG
1 TCATATCAG
30895392 TCA
1 TCA
30895395 ATTAGGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 13 0.52
9 12 0.48
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (9 bp):
TCATATCAG
Found at i:30904180 original size:28 final size:28
Alignment explanation
Indices: 30904148--30904226 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
30904138 GGAATATGGG
30904148 CCTTAGCCCATTTCAGTAACAGTGTGAA
1 CCTTAGCCCATTTCAGTAACAGTGTGAA
* * * **
30904176 CCTTAACCCAATAT-AGTAACAGCGTGGG
1 CCTTAGCCC-ATTTCAGTAACAGTGTGAA
* *
30904204 CCTTAGCCCAATACAGTAACAGT
1 CCTTAGCCCATTTCAGTAACAGT
30904227 ACAGTGCAGT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
27 1 0.03
28 35 0.90
29 3 0.08
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (28 bp):
CCTTAGCCCATTTCAGTAACAGTGTGAA
Found at i:30904634 original size:27 final size:26
Alignment explanation
Indices: 30904604--30904782 Score: 159
Period size: 27 Copynumber: 6.7 Consensus size: 26
30904594 TGACTCCTAA
*
30904604 GGGTATATT-AGTCATTTTACCCTATAG
1 GGGTAT-TTCAGTCATTTTACCCT-TGG
* *
30904631 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCAGTCATTTTACCCTT-GG
* * *
30904658 GGGTTTTTC-GATCATTTTACTCTTTG
1 GGGTATTTCAG-TCATTTTACCCTTGG
* *
30904684 GGGTGTTTCGGTCATTTTACCCTTCGG
1 GGGTATTTCAGTCATTTTACCCTT-GG
*
30904711 GGGTATTTCAATCATTTTACCCTTTGG
1 GGGTATTTCAGTCATTTTACCC-TTGG
*
30904738 GGGTATTT-TGATCATTTTACCCTTCGG
1 GGGTATTTCAG-TCATTTTACCCTT-GG
30904765 GGGTATTTC-GATCATTTT
1 GGGTATTTCAG-TCATTTT
30904783 CCCACAAATC
Statistics
Matches: 128, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
26 26 0.20
27 100 0.78
28 2 0.02
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (26 bp):
GGGTATTTCAGTCATTTTACCCTTGG
Found at i:30904697 original size:53 final size:53
Alignment explanation
Indices: 30904615--30904782 Score: 246
Period size: 54 Copynumber: 3.1 Consensus size: 53
30904605 GGTATATTAG
* * *
30904615 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTTTTTCGA
1 TCATTTTACCCT-TTGGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCGA
* * *
30904669 TCATTTTACTCTTTGGGGTGTTTCGGTCATTTTACCCTTCGGGGGTATTTCAA
1 TCATTTTACCCTTTGGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCGA
* *
30904722 TCATTTTACCCTTTGGGGGTATTTTGATCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTT-GGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCGA
30904776 TCATTTT
1 TCATTTT
30904783 CCCACAAATC
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
53 49 0.48
54 53 0.52
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (53 bp):
TCATTTTACCCTTTGGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCGA
Found at i:30904717 original size:80 final size:81
Alignment explanation
Indices: 30904614--30904782 Score: 218
Period size: 80 Copynumber: 2.1 Consensus size: 81
30904604 GGGTATATTA
**
30904614 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTTCGAGGGT-TTTTCGATCATTTTAC
1 GTCATTTTACCCTATAGGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTT-GATCATTTTAC
* * *
30904678 TCTT-TGGGGTGTTTCG
65 CCTTCGGGGGTATTTCG
* * *
30904694 GTCATTTTACCCT-TCGGGGGTATTTCAATCATTTTACCCTTTGGGGGTATTTTGATCATTTTAC
1 GTCATTTTACCCTAT-AGGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTTGATCATTTTAC
30904758 CCTTCGGGGGTATTTCG
65 CCTTCGGGGGTATTTCG
*
30904775 ATCATTTT
1 GTCATTTT
30904783 CCCACAAATC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 55 0.71
81 21 0.27
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (81 bp):
GTCATTTTACCCTATAGGGGTATTTCAATCATTTTACCCTTCGAGGGTATTTTGATCATTTTACC
CTTCGGGGGTATTTCG
Found at i:30907500 original size:28 final size:28
Alignment explanation
Indices: 30907469--30907547 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
30907459 GGAATGTGGG
*
30907469 CCTTAGCCCATTTCAGTAACATTGTGAA
1 CCTTAGCCCATTTCAGTAACAGTGTGAA
* * **
30907497 CCTTAACCCAATAT-AGTAACAGTGTGGG
1 CCTTAGCCC-ATTTCAGTAACAGTGTGAA
* *
30907525 CCTTAGCCCAATACAGTAACAGT
1 CCTTAGCCCATTTCAGTAACAGT
30907548 ACAGTGCAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 1 0.03
28 36 0.90
29 3 0.08
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (28 bp):
CCTTAGCCCATTTCAGTAACAGTGTGAA
Found at i:30909827 original size:28 final size:27
Alignment explanation
Indices: 30909795--30909865 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
30909785 TTAATAAGTA
30909795 CGCACACTTAGTGCTTAAT-AATCAAACT
1 CGCACACTTAGTGCTT--TCAATCAAACT
*
30909823 CGCACACTTAGTGCATTTCAATTAAACT
1 CGCACACTTAGTGC-TTTCAATCAAACT
*
30909851 CTCACACTTAGTGCT
1 CGCACACTTAGTGCT
30909866 AATCTCATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 2 0.05
28 35 0.90
29 2 0.05
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTTCAATCAAACT
Found at i:30910651 original size:27 final size:27
Alignment explanation
Indices: 30910634--30910974 Score: 398
Period size: 27 Copynumber: 12.6 Consensus size: 27
30910624 TATCCTATGG
30910634 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910661 GGGTATTTCGATCATTTTATCCTTCAA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910688 GGTTATTTCGGTCATTTTATCCTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910715 GGGTATTTAGGTCACTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
*
30910742 GGGTATTTCAGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910769 GGGTATTTCGATCATTTTATCCTT-TA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* *
30910795 GGGGTATTTCAGTCATTTTACCCTTCAA
1 -GGGTATTTCGGTCATTTTACCCTTCGA
*
30910823 GGGTATTTCGGTCATTTTACCCTTCAA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910850 GGGTATTTCGGTTATTTAACCC-TCCA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910876 GGGGTATTTCGGTAATTTTACCCTTTGG
1 -GGGTATTTCGGTCATTTTACCCTTCGA
* * *
30910904 GGGTATTTTGGTTATTTTACCCTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCGA
* *
30910931 GGGCATTTCGATCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
*
30910958 GGGTATTTCGATCATTT
1 GGGTATTTCGGTCATTT
30910975 GCCCACGAAT
Statistics
Matches: 267, Mismatches: 43, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
26 4 0.01
27 261 0.98
28 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTTCGA
Found at i:30915762 original size:44 final size:45
Alignment explanation
Indices: 30915634--30915781 Score: 142
Period size: 44 Copynumber: 3.3 Consensus size: 45
30915624 ATAAACAATG
* * ** *
30915634 TTCTCATTCTTTTCCCCGATGACACTTAATTCTTCACAATTTCCTTT
1 TTCTCATTCTTTTTCCCTATGAC-CTTTCTTCTTCCCAATTTCC-TT
* * **
30915681 TTCTTCTTTCTTTTT--CTGGTGATGTTTCTTCTTCCCAATTTCCTT
1 TTC-TCATTCTTTTTCCCT-ATGACCTTTCTTCTTCCCAATTTCCTT
*
30915726 TTCTC-TTCTTTTTCCCTATGACCTTTCTTCTTCCCAATTTCATT
1 TTCTCATTCTTTTTCCCTATGACCTTTCTTCTTCCCAATTTCCTT
30915770 TTCTC-TTCTTTT
1 TTCTCATTCTTTT
30915782 CTCTGCTAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
43 8 0.10
44 37 0.44
45 7 0.08
46 17 0.20
47 6 0.07
48 9 0.11
ACGTcount: A:0.11, C:0.28, G:0.05, T:0.55
Consensus pattern (45 bp):
TTCTCATTCTTTTTCCCTATGACCTTTCTTCTTCCCAATTTCCTT
Found at i:30924560 original size:224 final size:225
Alignment explanation
Indices: 30924158--30924609 Score: 897
Period size: 224 Copynumber: 2.0 Consensus size: 225
30924148 TTGACTCATA
30924158 TTTCTACAACGCCATCTTTGCTAAAGCCCGCCACGAACCTATCTTAAACTATGCAGGGAATTAAC
1 TTTCTACAACGCCATCTTTGCTAAAGCCCGCCACGAACCTATCTTAAACTATGCAGGGAATTAAC
30924223 TAAGTCGAATCTGTGCTTAGAAACTGGAAGACTTCTAGCCTTCGACTTATACATTGCCAAATCAA
66 TAAGTCGAATCTGTGCTTAGAAACTGGAAGACTTCTAGCCTTCGACTTATACATTGCCAAATCAA
30924288 AACTAACCCGGGTCTGATTTTCACTAACATAGTGCCTTAACTTTTCAAAGCCTGCATCCAAAAGA
131 AACTAACCCGGGTCTGATTTTCACTAACATAGTGCCTTAACTTTTCAAAGCCTGCATCCAAAAGA
30924353 GAATCTCTCTTCAACAAAACGGACATACAT
196 GAATCTCTCTTCAACAAAACGGACATACAT
30924383 TTTCTACAACG-CATCTTTGCTAAAGCCCGCCACGAACCTATCTTAAACTATGCAGGGAATTAAC
1 TTTCTACAACGCCATCTTTGCTAAAGCCCGCCACGAACCTATCTTAAACTATGCAGGGAATTAAC
30924447 TAAGTCGAATCTGTGCTTAGAAACTGGAAGACTTCTAGCCTTCGACTTATACATTGCCAAATCAA
66 TAAGTCGAATCTGTGCTTAGAAACTGGAAGACTTCTAGCCTTCGACTTATACATTGCCAAATCAA
30924512 AACTAACCCGGGTCTGATTTTCACTAACATAGTGCCTTAACTTTTCAAAGCCTGCATCCAAAAGA
131 AACTAACCCGGGTCTGATTTTCACTAACATAGTGCCTTAACTTTTCAAAGCCTGCATCCAAAAGA
30924577 GAATCTCTCTTCAACAAAACGGACATACAT
196 GAATCTCTCTTCAACAAAACGGACATACAT
30924607 TTT
1 TTT
30924610 TCCCTCCTAT
Statistics
Matches: 227, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
224 216 0.95
225 11 0.05
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (225 bp):
TTTCTACAACGCCATCTTTGCTAAAGCCCGCCACGAACCTATCTTAAACTATGCAGGGAATTAAC
TAAGTCGAATCTGTGCTTAGAAACTGGAAGACTTCTAGCCTTCGACTTATACATTGCCAAATCAA
AACTAACCCGGGTCTGATTTTCACTAACATAGTGCCTTAACTTTTCAAAGCCTGCATCCAAAAGA
GAATCTCTCTTCAACAAAACGGACATACAT
Found at i:30928365 original size:28 final size:28
Alignment explanation
Indices: 30928279--30928423 Score: 95
Period size: 28 Copynumber: 5.2 Consensus size: 28
30928269 ACACGTCAAA
* *
30928279 AAAGAATAGCCCTTGTGGCAAA-TCATG
1 AAAGAATAGCCTTTGTGGCAAATTCTTG
* * * *
30928306 AACGATTAGCCTATT-TGGCGAATT-TCG
1 AAAGAATAGCCT-TTGTGGCAAATTCTTG
*
30928333 AAAAGAATAGCCTTTGTGGTAAATATC-TG
1 -AAAGAATAGCCTTTGTGGCAAAT-TCTTG
* *
30928362 AAAGAAT-GGCTTGTGTGGCGAATTCTTG
1 AAAGAATAGCCTT-TGTGGCAAATTCTTG
* *
30928390 AACGAATAGCCCTTGTGGCAAGATT-TTG
1 AAAGAATAGCCTTTGTGGCAA-ATTCTTG
*
30928418 GAAGAA
1 AAAGAA
30928424 AACGCCTTGG
Statistics
Matches: 88, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
27 24 0.27
28 56 0.64
29 8 0.09
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (28 bp):
AAAGAATAGCCTTTGTGGCAAATTCTTG
Found at i:30940473 original size:19 final size:19
Alignment explanation
Indices: 30940449--30940487 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30940439 CATTTAATTT
30940449 GGTGCCCCTATTATCTCAG
1 GGTGCCCCTATTATCTCAG
30940468 GGTGCCCCTATTATCTCAG
1 GGTGCCCCTATTATCTCAG
30940487 G
1 G
30940488 CTGTACCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (19 bp):
GGTGCCCCTATTATCTCAG
Found at i:30944724 original size:2 final size:2
Alignment explanation
Indices: 30944717--30944748 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30944707 ACCTATTAGA
30944717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30944749 CTTCCGAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30945036 original size:47 final size:48
Alignment explanation
Indices: 30944939--30945036 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
30944929 CACCGATGAG
30944939 ATCACCATTTTTAATAGCCATCACACCATCTTCTCCATTACTGCTGCA
1 ATCACCATTTTTAATAGCCATCACACCATCTTCTCCATTACTGCTGCA
30944987 ATCACCATTTTTAATAGCCATCACACC-TCTTCTCCATTACTGCTGCA
1 ATCACCATTTTTAATAGCCATCACACCATCTTCTCCATTACTGCTGCA
30945034 ATC
1 ATC
30945037 CTGAAACAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 23 0.46
48 27 0.54
ACGTcount: A:0.27, C:0.34, G:0.06, T:0.34
Consensus pattern (48 bp):
ATCACCATTTTTAATAGCCATCACACCATCTTCTCCATTACTGCTGCA
Found at i:30947801 original size:14 final size:14
Alignment explanation
Indices: 30947782--30947810 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30947772 TGGAATTATG
30947782 TTTATTGTTATTGT
1 TTTATTGTTATTGT
30947796 TTTATTGTTATTGT
1 TTTATTGTTATTGT
30947810 T
1 T
30947811 ACATTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (14 bp):
TTTATTGTTATTGT
Found at i:30959523 original size:45 final size:45
Alignment explanation
Indices: 30959297--30959526 Score: 309
Period size: 45 Copynumber: 5.1 Consensus size: 45
30959287 GGAGTAGGTT
*
30959297 GAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
30959342 GAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
30959387 GATA-ATAGCAGATCTTGTCTTGCTGTATTGGCAGTGAAGTGGATC
1 GA-AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
30959432 GAAGATAGCATATCTTATCTTCCTATTTTGGCAACGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
30959477 GAAGATAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
30959522 GAAGA
1 GAAGA
30959527 CACTAGCCTT
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 158 0.99
46 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:30959525 original size:90 final size:90
Alignment explanation
Indices: 30959297--30959607 Score: 310
Period size: 90 Copynumber: 3.5 Consensus size: 90
30959287 GGAGTAGGTT
* * * * * * * *
30959297 GAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAAATAGCAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCGAAGATAGCATATCTTGTCT
*
30959362 TCCTGTATTGGCAGCGAAGTAGATC
66 TCCTATATTGGCAGCGAAGTAGATC
* * * *** *
30959387 GATA-ATAGCAGATCTTGTCTTGCTGTATTGGCAGTGAAGTGGATCGAAGATAGCATATCTTATC
1 GA-AGATAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCGAAGATAGCATATCTTGTC
* *
30959451 TTCCTATTTTGGCAACGAAGTAGATC
65 TTCCTATATTGGCAGCGAAGTAGATC
* *
30959477 GAAGATAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCGAAGACA-C-TAGCCTTGTC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCGAAGATAGCATA-TCTTGTC
* *
30959540 TCCCTA-AGCTT-GCAGCGGAGTAGA-C
65 TTCCTATA--TTGGCAGCGAAGTAGATC
* * *
30959565 TAAAAGCAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAA
1 GAAGA-TAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAA
30959608 GTCAAAAACA
Statistics
Matches: 189, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
88 6 0.03
89 59 0.31
90 123 0.65
91 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (90 bp):
GAAGATAGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCGAAGATAGCATATCTTGTCT
TCCTATATTGGCAGCGAAGTAGATC
Found at i:30959631 original size:89 final size:88
Alignment explanation
Indices: 30959483--30959650 Score: 239
Period size: 89 Copynumber: 1.9 Consensus size: 88
30959473 GATCGAAGAT
* * * *
30959483 AGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCGAAGACACTAGCCTTGTCTCCCTAAG
1 AGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCAAAAACACCAGCCTTATCTCCCTAAG
*
30959548 CTTGCAGCGGAGTAGACTAAAAGC
66 -TAGCAGCGGAGTAGACTAAAAGC
* *
30959572 AGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAGTCAAAAACACCAGTCC-TATCTCCCTGA
1 AGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCAAAAACACCAG-CCTTATCTCCCTAA
*
30959636 GTAGCAGTGGAGTAG
65 GTAGCAGCGGAGTAG
30959651 GTTGAAGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
88 12 0.17
89 56 0.80
90 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCCTGTACTAGCAGTGAAGCAAATCAAAAACACCAGCCTTATCTCCCTAAG
TAGCAGCGGAGTAGACTAAAAGC
Found at i:30960034 original size:44 final size:44
Alignment explanation
Indices: 30959961--30960241 Score: 144
Period size: 44 Copynumber: 6.2 Consensus size: 44
30959951 TAAAGATACC
* ** *
30959961 AATCTTATCTCCCTGAAGTTATGGCGGAGCAGATTGAAGCTACT
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACT
* * * * *
30960005 AATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAAACGA-T
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACT
* * *
30960048 GAATCCTATAC-CTCTGAAGTTACAGTAGG-TCAAATT-AAGTCTATCAT
1 -AATCCTAT-CTCCCTGAAGTTACAGT-GGAGCAGATTGAAG-CTA-C-T
* * * * * *
30960095 AACAAGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAAGATAACCAC
1 ---AA-TCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCT-A-C-T
* * * * *
30960146 AAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTG-A--TACC
1 AATCC-TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACT
* * * *
30960188 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCTATT
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACT
30960232 AATCCTATCT
1 AATCCTATCT
30960242 ATTTGAAGTT
Statistics
Matches: 178, Mismatches: 41, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
41 28 0.16
42 5 0.03
43 4 0.02
44 72 0.40
45 4 0.02
47 3 0.02
48 29 0.16
49 5 0.03
50 22 0.12
51 6 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACT
Found at i:30960412 original size:227 final size:224
Alignment explanation
Indices: 30959955--30960402 Score: 531
Period size: 227 Copynumber: 2.0 Consensus size: 224
30959945 TCAAGTTAAA
** * *
30959955 GATACCAATCTTATCTCCCTGAAGTTATGGCGGAGCAGATTGAAGCTACTAATCCTATCTCCCTA
1 GATACCAATCTTATCTCCCTGAAGTTACAGCAGAGCAGATTGAAGCTACTAATCCTATCTACCTA
* * * **
30960020 AAGTTACAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTACAGTAGGTCAAATTA
66 AAGTTACAGTAGAGAGGATTAAAACGATGAATCCTATACCTCTAAAGTTACAAAAGGTCAAATTA
* * * * * *
30960085 AGTCTATCATAACAAGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAAGATAACCACAAAC
131 A---TATAATAACAAATCTTATCTCCCTAAAGATGCAGTGGAGCAGACTGAAGACAACCACAAAC
30960150 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTT
193 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTT
* * * ** *
30960182 GATACCAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCTATTAATCCTATCTATTTG
1 GATACCAATCTTATCTCCCTGAAGTTACAGCAGAGCAGATTGAAGCTACTAATCCTATCTACCTA
* * * * **
30960247 AAGTTGCAGTAGAGAGGATTAAAACGATGAATCTTATACCTCTAAATTTGCAAAAGGTCGGATTA
66 AAGTTACAGTAGAGAGGATTAAAACGATGAATCCTATACCTCTAAAGTTACAAAAGGTCAAATTA
* * * * **
30960312 A-A-AATAACAAAATCTTATCTCCCTAAAGATGTAGTGGAGCAGATTGAAGACCGACTACAAGTC
131 ATATAATAAC-AAATCTTATCTCCCTAAAGATGCAGTGGAGCAGACTGAAGA-CAACCACAAACC
*
30960375 TTATCTCCCTAAAGTTGTAGTGGAGCAG
194 TTATCTCCCTAAAGTTGCAGTGGAGCAG
30960403 ATCGTTGATA
Statistics
Matches: 185, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
222 5 0.03
223 36 0.19
224 34 0.18
227 110 0.59
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (224 bp):
GATACCAATCTTATCTCCCTGAAGTTACAGCAGAGCAGATTGAAGCTACTAATCCTATCTACCTA
AAGTTACAGTAGAGAGGATTAAAACGATGAATCCTATACCTCTAAAGTTACAAAAGGTCAAATTA
ATATAATAACAAATCTTATCTCCCTAAAGATGCAGTGGAGCAGACTGAAGACAACCACAAACCTT
ATCTCCCTAAAGTTGCAGTGGAGCAGGTT
Found at i:30960754 original size:22 final size:22
Alignment explanation
Indices: 30960726--30960806 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
30960716 TGACCCGGGG
30960726 CCCAATACCCCAACTAAACCTA
1 CCCAATACCCCAACTAAACCTA
* *
30960748 CCCAATA-CCCAAATAACCCATTACA
1 CCCAATACCCCAACTAAACC--T--A
30960773 GGCCCAATACCCCAACTAAACCTA
1 --CCCAATACCCCAACTAAACCTA
*
30960797 CCTAATACCC
1 CCCAATACCC
30960807 AAATAACCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
21 10 0.21
22 16 0.34
23 1 0.02
24 1 0.02
25 1 0.02
26 1 0.02
27 7 0.15
28 10 0.21
ACGTcount: A:0.40, C:0.43, G:0.02, T:0.15
Consensus pattern (22 bp):
CCCAATACCCCAACTAAACCTA
Found at i:30961197 original size:16 final size:15
Alignment explanation
Indices: 30961168--30961205 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
30961158 GTATGAGATC
30961168 TATTTTT-GTTTTTT
1 TATTTTTCGTTTTTT
30961182 TATTTTTCGATTTTTT
1 TATTTTTCG-TTTTTT
30961198 TATTTTTC
1 TATTTTTC
30961206 TTCCCTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 7 0.32
15 1 0.05
16 14 0.64
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.79
Consensus pattern (15 bp):
TATTTTTCGTTTTTT
Found at i:30962065 original size:14 final size:14
Alignment explanation
Indices: 30962046--30962074 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30962036 TGGAATTATG
30962046 TTTATTGTTATTGT
1 TTTATTGTTATTGT
30962060 TTTATTGTTATTGT
1 TTTATTGTTATTGT
30962074 T
1 T
30962075 ACATTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (14 bp):
TTTATTGTTATTGT
Found at i:30964879 original size:14 final size:15
Alignment explanation
Indices: 30964860--30964891 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
30964850 TACAAGAAAC
30964860 AAAAATCAAATA-AT
1 AAAAATCAAATATAT
30964874 AAAAATCAAATATAT
1 AAAAATCAAATATAT
30964889 AAA
1 AAA
30964892 TTAATAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAATCAAATATAT
Found at i:30967011 original size:16 final size:16
Alignment explanation
Indices: 30966990--30967025 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30966980 AGACGAAAAA
* *
30966990 GAAAGAAAGGAAAGGG
1 GAAAGAAAAGAAAAGG
30967006 GAAAGAAAAGAAAAGG
1 GAAAGAAAAGAAAAGG
30967022 GAAA
1 GAAA
30967026 AACTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAAGG
Found at i:30967479 original size:40 final size:40
Alignment explanation
Indices: 30967435--30967512 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
30967425 AATTGAATCG
* *
30967435 AAGTGAAATT-ATTTGAACTGTGTATTGACTAGAAAGTGGA
1 AAGTGAAATTGAATTGAACTGTG-ATTGAATAGAAAGTGGA
* *
30967475 AAGTGAAATTGAATTGAATTGTGATTGAATTGAAAGTG
1 AAGTGAAATTGAATTGAACTGTGATTGAATAGAAAGTG
30967513 AATTTGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 23 0.70
41 10 0.30
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (40 bp):
AAGTGAAATTGAATTGAACTGTGATTGAATAGAAAGTGGA
Found at i:30976238 original size:13 final size:13
Alignment explanation
Indices: 30976220--30976245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30976210 TAAGTAAAAC
30976220 TATTATATTATTA
1 TATTATATTATTA
30976233 TATTATATTATTA
1 TATTATATTATTA
30976246 GAAAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:30976951 original size:21 final size:20
Alignment explanation
Indices: 30976927--30976986 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
30976917 TATCGTGCCG
30976927 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCAC-TTATGTGTCGT
**
30976948 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCA-CTTATGTGTCGT
*
30976969 TTCAGGCACTTATGTGTC
1 ATCAGGCACTTATGTGTC
30976987 TTATACTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 8 0.24
21 24 0.73
22 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (20 bp):
ATCAGGCACTTATGTGTCGT
Found at i:30991747 original size:9 final size:9
Alignment explanation
Indices: 30991733--30991763 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30991723 GTTAAACGAA
30991733 TCGAGTTAT
1 TCGAGTTAT
*
30991742 TCGAGTTAA
1 TCGAGTTAT
30991751 TCGAGTTAT
1 TCGAGTTAT
30991760 TCGA
1 TCGA
30991764 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:30991834 original size:9 final size:9
Alignment explanation
Indices: 30991817--30991853 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30991807 TGAGTCTTCG
30991817 AATTCGAAT
1 AATTCGAAT
*
30991826 AACTCGAAT
1 AATTCGAAT
30991835 AATTCGAAT
1 AATTCGAAT
30991844 AATTCGAAT
1 AATTCGAAT
30991853 A
1 A
30991854 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:30993078 original size:18 final size:16
Alignment explanation
Indices: 30993057--30993099 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
30993047 AAATACAGTG
30993057 TTTTATTATAATAATTAA
1 TTTT-TTATAA-AATTAA
*
30993075 TTTTGTTGTAAAATTAA
1 TTTT-TTATAAAATTAA
30993092 TTTTTTAT
1 TTTTTTAT
30993100 GTTTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTTATAAAATTAA
Found at i:30993451 original size:21 final size:20
Alignment explanation
Indices: 30993425--30993467 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
30993415 TGTGATTTAA
30993425 ATCTCAAATATTATTACAAAT
1 ATCTCAAATATTA-TACAAAT
*
30993446 ATCTCAAATATTATATAAAT
1 ATCTCAAATATTATACAAAT
30993466 AT
1 AT
30993468 ATAACAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
ATCTCAAATATTATACAAAT
Found at i:30996245 original size:15 final size:14
Alignment explanation
Indices: 30996213--30996258 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
30996203 AAGATGTGAA
30996213 TTTAATTTATATAT
1 TTTAATTTATATAT
30996227 TTTAATTTGAT-TAAT
1 TTTAATTT-ATAT-AT
30996242 TTTAATCTT-TATAT
1 TTTAAT-TTATATAT
30996256 TTT
1 TTT
30996259 TTGAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 15 0.54
15 11 0.39
16 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTAATTTATATAT
Found at i:31006053 original size:22 final size:23
Alignment explanation
Indices: 31006000--31006055 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
31005990 CCCGTTTTTA
* * *
31006000 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
31006023 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
31006045 ATTAAAATTAA
1 ATTAAAATTAA
31006056 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:31006068 original size:16 final size:16
Alignment explanation
Indices: 31006031--31006070 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
31006021 TTAATAAAAT
* *
31006031 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
31006047 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
31006063 TAAAATTA
1 TAAAATTA
31006071 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:31006181 original size:68 final size:68
Alignment explanation
Indices: 31006059--31006268 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
31006049 AAATTAATTG
*
31006059 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
31006122 TGA
66 TGA
*
31006125 TTAGTAAATTTATCAAATTATTAATTGTATTAATTATATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
31006190 TGA
66 TGA
*
31006193 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
31006258 TGA
66 TGA
31006261 TTAGTAAA
1 TTAGTAAA
31006269 ACAAACTTGA
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 26 0.19
68 112 0.81
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:31006223 original size:9 final size:9
Alignment explanation
Indices: 31006211--31006238 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
31006201 TTTATCAAAT
31006211 TATTAATTG
1 TATTAATTG
31006220 TATTAATTG
1 TATTAATTG
31006229 TATTAATTG
1 TATTAATTG
31006238 T
1 T
31006239 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:31006375 original size:22 final size:24
Alignment explanation
Indices: 31006335--31006378 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
31006325 AAATAAACTT
31006335 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
31006359 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
31006379 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:31031932 original size:64 final size:63
Alignment explanation
Indices: 31031831--31031954 Score: 203
Period size: 64 Copynumber: 2.0 Consensus size: 63
31031821 TCCCACTGCT
* * *
31031831 AAATAAGAAGGCATTATTCTTCAGTTTAGCCAAAGCTAAAGTCTATTCCAAATTTGATCTCGCC
1 AAATAAGAAGGCATTATTATCCAATTTAGCCAAAGCT-AAGTCTATTCCAAATTTGATCTCGCC
*
31031895 AAATAAGAAGGCATTATTATCCAATTTAGTCAAAGCTAAGTCTATTCCAAATTTGATCTC
1 AAATAAGAAGGCATTATTATCCAATTTAGCCAAAGCTAAGTCTATTCCAAATTTGATCTC
31031955 AAAGCTATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
63 23 0.41
64 33 0.59
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (63 bp):
AAATAAGAAGGCATTATTATCCAATTTAGCCAAAGCTAAGTCTATTCCAAATTTGATCTCGCC
Found at i:31034665 original size:69 final size:70
Alignment explanation
Indices: 31034591--31034744 Score: 170
Period size: 69 Copynumber: 2.2 Consensus size: 70
31034581 TGACCTAGGA
* *
31034591 GAAAAAATAAAATTATGTAATAAATATAACTATA-AAATTTTAATAT-AAAAAACAAATGA-ATT
1 GAAAAAATAAAATTATCTAACAAATATAACTATAGAAA-TTTAATATAAAAAAACAAATGAGA-T
31034653 TTTAGTT
64 TTTAGTT
* ** ** * *
31034660 TAAAAAATAGCATTATCTAACAAATATATGTATAGAAATTTGATATAAAAAAATAAATGAGATTT
1 GAAAAAATAAAATTATCTAACAAATATAACTATAGAAATTTAATATAAAAAAACAAATGAGATTT
31034725 TAGTT
66 TAGTT
*
31034730 GAAATAAGTAAAATT
1 GAAA-AAATAAAATT
31034745 TAATATAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
69 34 0.50
70 26 0.38
71 8 0.12
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (70 bp):
GAAAAAATAAAATTATCTAACAAATATAACTATAGAAATTTAATATAAAAAAACAAATGAGATTT
TAGTT
Found at i:31037051 original size:2 final size:2
Alignment explanation
Indices: 31037044--31037146 Score: 95
Period size: 2 Copynumber: 51.5 Consensus size: 2
31037034 CTATTCCAAC
* *
31037044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
31037086 -T A- ACT AT AT TT AT A- AT AG AT CT CACC AC AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT
31037126 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
31037147 AACATATTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
1 3 0.04
2 79 0.94
3 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31037153 original size:68 final size:68
Alignment explanation
Indices: 31037046--31037180 Score: 252
Period size: 68 Copynumber: 2.0 Consensus size: 68
31037036 ATTCCAACAT
*
31037046 ATATATATATATATATATATATATATATATATAAACATATTAACTATATTTATAATAGATCTCAC
1 ATATATATATATATATATATATATATATATATAAACATATTAACTAAATTTATAATAGATCTCAC
31037111 CAC
66 CAC
*
31037114 ATATATATATATATATATATATATATATATATAAACATATTAACTAAATTTATAATCGATCTCAC
1 ATATATATATATATATATATATATATATATATAAACATATTAACTAAATTTATAATAGATCTCAC
31037179 CA
66 CA
31037181 ACCATTTCCT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.41
Consensus pattern (68 bp):
ATATATATATATATATATATATATATATATATAAACATATTAACTAAATTTATAATAGATCTCAC
CAC
Found at i:31046492 original size:30 final size:30
Alignment explanation
Indices: 31046457--31046515 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
31046447 AATAATAACA
31046457 TTTTTTGAA-ATAATATGTTGACTTTATTTT
1 TTTTTTGAACA-AATATGTTGACTTTATTTT
*
31046487 TTTTTTGAACGAAATATGTTGGCTTTATT
1 TTTTTTGAAC-AAATATGTTGACTTTATT
31046516 AATAATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.35
31 16 0.62
32 1 0.04
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (30 bp):
TTTTTTGAACAAATATGTTGACTTTATTTT
Found at i:31047091 original size:13 final size:13
Alignment explanation
Indices: 31047073--31047097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31047063 TCTTTTAAAA
31047073 TTTTACAATTTTT
1 TTTTACAATTTTT
31047086 TTTTACAATTTT
1 TTTTACAATTTT
31047098 ATCAAATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTACAATTTTT
Found at i:31053418 original size:354 final size:354
Alignment explanation
Indices: 31052769--31053478 Score: 1420
Period size: 354 Copynumber: 2.0 Consensus size: 354
31052759 GGACTGACAG
31052769 TATATTGGACAGGACCTAAGAAAAATAGATCTTGAATCTATTTATGATTTATTCACTTGTGATGT
1 TATATTGGACAGGACCTAAGAAAAATAGATCTTGAATCTATTTATGATTTATTCACTTGTGATGT
31052834 TCATAATGTCGCATACATAAATCCTAAGTGGATGACAGACTATGTATGCGTGACTCGTACACTTT
66 TCATAATGTCGCATACATAAATCCTAAGTGGATGACAGACTATGTATGCGTGACTCGTACACTTT
31052899 GATGTAAGTAAAAGCCTGAGTTCGGATTGATAAGGAAACGAAAGTCAGTGCGTTTGGTGTACAAC
131 GATGTAAGTAAAAGCCTGAGTTCGGATTGATAAGGAAACGAAAGTCAGTGCGTTTGGTGTACAAC
31052964 TTTTGCAGTATGTGGCGTCATTCACAATAGTGAAATTCATAACTCGAGACATGGGTAAATGATAT
196 TTTTGCAGTATGTGGCGTCATTCACAATAGTGAAATTCATAACTCGAGACATGGGTAAATGATAT
31053029 CCTCTAATTGGCATTACATGGTTGATGAAAAGTAAACATGGCCATGGACCATTTGTCTTTGTAAT
261 CCTCTAATTGGCATTACATGGTTGATGAAAAGTAAACATGGCCATGGACCATTTGTCTTTGTAAT
31053094 GAATGACTTGATTACTATTTGATAGTAAT
326 GAATGACTTGATTACTATTTGATAGTAAT
31053123 TATATTGGACAGGACCTAAGAAAAATAGATCTTGAATCTATTTATGATTTATTCACTTGTGATGT
1 TATATTGGACAGGACCTAAGAAAAATAGATCTTGAATCTATTTATGATTTATTCACTTGTGATGT
31053188 TCATAATGTCGCATACATAAATCCTAAGTGGATGACAGACTATGTATGCGTGACTCGTACACTTT
66 TCATAATGTCGCATACATAAATCCTAAGTGGATGACAGACTATGTATGCGTGACTCGTACACTTT
31053253 GATGTAAGTAAAAGCCTGAGTTCGGATTGATAAGGAAACGAAAGTCAGTGCGTTTGGTGTACAAC
131 GATGTAAGTAAAAGCCTGAGTTCGGATTGATAAGGAAACGAAAGTCAGTGCGTTTGGTGTACAAC
31053318 TTTTGCAGTATGTGGCGTCATTCACAATAGTGAAATTCATAACTCGAGACATGGGTAAATGATAT
196 TTTTGCAGTATGTGGCGTCATTCACAATAGTGAAATTCATAACTCGAGACATGGGTAAATGATAT
31053383 CCTCTAATTGGCATTACATGGTTGATGAAAAGTAAACATGGCCATGGACCATTTGTCTTTGTAAT
261 CCTCTAATTGGCATTACATGGTTGATGAAAAGTAAACATGGCCATGGACCATTTGTCTTTGTAAT
31053448 GAATGACTTGATTACTATTTGATAGTAAT
326 GAATGACTTGATTACTATTTGATAGTAAT
31053477 TA
1 TA
31053479 ACTTTTTATA
Statistics
Matches: 356, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 356 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (354 bp):
TATATTGGACAGGACCTAAGAAAAATAGATCTTGAATCTATTTATGATTTATTCACTTGTGATGT
TCATAATGTCGCATACATAAATCCTAAGTGGATGACAGACTATGTATGCGTGACTCGTACACTTT
GATGTAAGTAAAAGCCTGAGTTCGGATTGATAAGGAAACGAAAGTCAGTGCGTTTGGTGTACAAC
TTTTGCAGTATGTGGCGTCATTCACAATAGTGAAATTCATAACTCGAGACATGGGTAAATGATAT
CCTCTAATTGGCATTACATGGTTGATGAAAAGTAAACATGGCCATGGACCATTTGTCTTTGTAAT
GAATGACTTGATTACTATTTGATAGTAAT
Found at i:31053914 original size:57 final size:56
Alignment explanation
Indices: 31053835--31053963 Score: 161
Period size: 57 Copynumber: 2.3 Consensus size: 56
31053825 AAAAATGGTG
* * * *
31053835 AAATAGAGAAATAAGAAGCATTTGGAAATGATTAAGGTTTTCTCCAAAATGAAAATGA
1 AAAT-GAGAAATGA-AAGCATTTGGAAATAAATAAGATTTTCTCCAAAATGAAAATGA
* **
31053893 AAATGGAGAAATGAAATCATTTGGAAATAAATGTGATTTTCTCCAAAATGAAAATGA
1 AAAT-GAGAAATGAAAGCATTTGGAAATAAATAAGATTTTCTCCAAAATGAAAATGA
31053950 AAATGA-AAATGAAA
1 AAATGAGAAATGAAA
31053964 ATAAAAATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 8 0.13
56 2 0.03
57 41 0.65
58 12 0.19
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (56 bp):
AAATGAGAAATGAAAGCATTTGGAAATAAATAAGATTTTCTCCAAAATGAAAATGA
Found at i:31053948 original size:6 final size:6
Alignment explanation
Indices: 31053937--31053981 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
31053927 GATTTTCTCC
*
31053937 AAAATG AAAATG AAAATG AAAATG AAAATA AAAATG AAAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG -AAAATG AA
31053982 TTTATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:31055823 original size:41 final size:41
Alignment explanation
Indices: 31055779--31055913 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 41
31055769 GACTGCGAGT
*
31055779 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* * * *
31055820 CGATGAGGCACTGCGTGCCAA-TT-C-ACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* **
31055857 CGATGAGACACTGGGTGTC-ATATTATTACTTCAAATT-ATC
1 CGATGAGACACTGGGTGTCAAT-TTACTACTTCGGATTAATC
*
31055897 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
31055914 CCAAACTGGT
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
36 1 0.01
37 16 0.21
38 13 0.17
39 2 0.03
40 26 0.34
41 18 0.24
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (41 bp):
CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
Found at i:31057609 original size:29 final size:29
Alignment explanation
Indices: 31057567--31057625 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
31057557 GAATATAAAC
*
31057567 TATATTTTTTATTTTTAAAATATACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
31057596 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
31057625 T
1 T
31057626 TTAATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:31057635 original size:29 final size:29
Alignment explanation
Indices: 31057574--31057635 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
31057564 AACTATATTT
* * *
31057574 TTTATTTTTAAAATATACTACATATATTT
1 TTTATTTTTAAAATACACTACATATAATA
*
31057603 TTTATTTTTAAAATACACTACATTTAATA
1 TTTATTTTTAAAATACACTACATATAATA
31057632 TTTA
1 TTTA
31057636 AAACAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTATTTTTAAAATACACTACATATAATA
Found at i:31063900 original size:10 final size:10
Alignment explanation
Indices: 31063880--31063914 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
31063870 AAGGGTAAGG
31063880 GGGAGGGGAGA
1 GGGA-GGGAGA
31063891 GGGAGGGAGA
1 GGGAGGGAGA
31063901 GGGAGGGAGA
1 GGGAGGGAGA
31063911 GGGA
1 GGGA
31063915 TGGGTTGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (10 bp):
GGGAGGGAGA
Found at i:31064840 original size:22 final size:22
Alignment explanation
Indices: 31064815--31064856 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31064805 AAAAATATAT
*
31064815 TTTCTTTTTTAAATATATAAGC
1 TTTCCTTTTTAAATATATAAGC
31064837 TTTCCTTTTTAAATATATAA
1 TTTCCTTTTTAAATATATAA
31064857 TATGACCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTCCTTTTTAAATATATAAGC
Found at i:31066112 original size:22 final size:22
Alignment explanation
Indices: 31066068--31066113 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31066058 TTCTCCTTGT
* *
31066068 CAGGCATCGGTATTGCGATACC
1 CAGGCATCGGTATTGCAACACC
31066090 CAGGC-TCTGGTATTGCAACACC
1 CAGGCATC-GGTATTGCAACACC
31066112 CA
1 CA
31066114 CGTTAGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (22 bp):
CAGGCATCGGTATTGCAACACC
Found at i:31066557 original size:19 final size:20
Alignment explanation
Indices: 31066535--31066572 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31066525 AAAAATTAAT
31066535 AAAACAAAAAAATT-TAAAC
1 AAAACAAAAAAATTGTAAAC
*
31066554 AAAATAAAAAAATTGTAAA
1 AAAACAAAAAAATTGTAAA
31066573 AAATGTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAACAAAAAAATTGTAAAC
Found at i:31066565 original size:27 final size:27
Alignment explanation
Indices: 31066513--31066565 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31066503 AAAAATTTTA
* *
31066513 AAAAAAATTGTAAAAAATTAATAAAAC
1 AAAAAAATTGTAAAAAAATAAAAAAAC
31066540 AAAAAAATT-TAAACAAAATAAAAAAA
1 AAAAAAATTGTAAA-AAAATAAAAAAA
31066566 TTGTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (27 bp):
AAAAAAATTGTAAAAAAATAAAAAAAC
Found at i:31068911 original size:55 final size:55
Alignment explanation
Indices: 31068834--31068938 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
31068824 AATGCTGCTC
*
31068834 AACTCTATGTTTGTTCTACATCATTTCAACTCTAAAATACTCAAGGAGATGAAAA
1 AACTCGATGTTTGTTCTACATCATTTCAACTCTAAAATACTCAAGGAGATGAAAA
* *
31068889 AACTCGATG-TTGATTCTGCATCATTTCAACTCTAAAATACTCAATGAGAT
1 AACTCGATGTTTG-TTCTACATCATTTCAACTCTAAAATACTCAAGGAGAT
31068939 AAGATTCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 3 0.07
55 43 0.93
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (55 bp):
AACTCGATGTTTGTTCTACATCATTTCAACTCTAAAATACTCAAGGAGATGAAAA
Found at i:31074954 original size:10 final size:10
Alignment explanation
Indices: 31074939--31074963 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31074929 AGTTTACTCA
31074939 AAAAAAAAAG
1 AAAAAAAAAG
31074949 AAAAAAAAAG
1 AAAAAAAAAG
31074959 AAAAA
1 AAAAA
31074964 GAACAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:31079692 original size:6 final size:6
Alignment explanation
Indices: 31079683--31079708 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31079673 CAAAATAAAT
31079683 AATTTA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
31079709 ATATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:31081226 original size:11 final size:11
Alignment explanation
Indices: 31081196--31081234 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31081186 CATGATTATG
31081196 TACATAAAAGTA
1 TACATAAAA-TA
*
31081208 TCCATAAAATA
1 TACATAAAATA
31081219 TACATAAAA-A
1 TACATAAAATA
31081229 TACATA
1 TACATA
31081235 TGACAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 7 0.28
11 10 0.40
12 8 0.32
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (11 bp):
TACATAAAATA
Found at i:31081584 original size:2 final size:2
Alignment explanation
Indices: 31081579--31081604 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31081569 GGTATACATC
31081579 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31081605 GACAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31087760 original size:87 final size:87
Alignment explanation
Indices: 31087609--31087784 Score: 298
Period size: 87 Copynumber: 2.0 Consensus size: 87
31087599 GACGAATTGG
* *
31087609 ACACCACTTACCTTTATCAATTTTTGCGTGAATAATATGCCCTAACCATTCCATATATAACACAA
1 ACACCACTTACCTTTATCAATTTTTGCGTGAATAATATGCCCTAACCATTCCACACATAACACAA
*
31087674 AAAGGTAAGGTGGTAATGGACA
66 AAAGGTAAGGTGATAATGGACA
* * *
31087696 ACACCACTTACCTTTATCAATTTTTGTGTGAATAATGTGCCCTAACCATTCCACACATAGCACAA
1 ACACCACTTACCTTTATCAATTTTTGCGTGAATAATATGCCCTAACCATTCCACACATAACACAA
31087761 AAAGGTAAGGTGATAATGGACA
66 AAAGGTAAGGTGATAATGGACA
31087783 AC
1 AC
31087785 CTTGTCTGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (87 bp):
ACACCACTTACCTTTATCAATTTTTGCGTGAATAATATGCCCTAACCATTCCACACATAACACAA
AAAGGTAAGGTGATAATGGACA
Found at i:31087995 original size:14 final size:15
Alignment explanation
Indices: 31087976--31088004 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31087966 CAACATGATC
31087976 ACCATC-CATTTTTT
1 ACCATCTCATTTTTT
31087990 ACCATCTCATTTTTT
1 ACCATCTCATTTTTT
31088005 TCGCATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.52
Consensus pattern (15 bp):
ACCATCTCATTTTTT
Found at i:31095428 original size:10 final size:10
Alignment explanation
Indices: 31095413--31095459 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
31095403 TAAAATTTTG
31095413 AATTTTAATT
1 AATTTTAATT
31095423 AATTTTACAATT
1 AATTTT--AATT
*
31095435 AATTTTGATT
1 AATTTTAATT
*
31095445 AATTTTGATT
1 AATTTTAATT
31095455 -ATTTT
1 AATTTT
31095460 CGACAGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.15
10 19 0.56
12 10 0.29
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (10 bp):
AATTTTAATT
Found at i:31099108 original size:21 final size:22
Alignment explanation
Indices: 31099082--31099124 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
31099072 ATTGTAGTTC
* *
31099082 TGTTGTTGATTGTAATT-CCCT
1 TGTTGTGGATTATAATTGCCCT
31099103 TGTTGTGGATTATAATTGCCCT
1 TGTTGTGGATTATAATTGCCCT
31099125 GAGTAGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (22 bp):
TGTTGTGGATTATAATTGCCCT
Found at i:31115386 original size:7 final size:7
Alignment explanation
Indices: 31115374--31115409 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
31115364 ATTGTTTTAT
31115374 TTTAATA
1 TTTAATA
31115381 TTTAATAA
1 TTTAAT-A
*
31115389 TTTTATA
1 TTTAATA
31115396 TTTAATA
1 TTTAATA
31115403 TTTAATA
1 TTTAATA
31115410 ATTTTATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAATA
Found at i:31115398 original size:15 final size:15
Alignment explanation
Indices: 31115372--31115430 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
31115362 ATATTGTTTT
31115372 ATTTTAATATTTAATA
1 ATTTT-ATATTTAATA
31115388 ATTTTATATTTAAT-
1 ATTTTATATTTAATA
* *
31115402 ATTTAATAATTTTATA
1 ATTTTAT-ATTTAATA
*
31115418 CATTTTTTATTTA
1 -ATTTTATATTTA
31115431 TTGAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.17
15 15 0.43
16 9 0.26
17 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTATATTTAATA
Found at i:31115401 original size:22 final size:22
Alignment explanation
Indices: 31115368--31115417 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
31115358 AAATATATTG
31115368 TTTTAT-TTTAATATTTAATAA
1 TTTTATATTTAATATTTAATAA
31115389 TTTTATATTTAATATTTAATAA
1 TTTTATATTTAATATTTAATAA
31115411 TTTTATA
1 TTTTATA
31115418 CATTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTATATTTAATATTTAATAA
Found at i:31116654 original size:7 final size:7
Alignment explanation
Indices: 31116642--31116677 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
31116632 ATTGTTTTAT
31116642 TTTAATA
1 TTTAATA
31116649 TTTAATAA
1 TTTAAT-A
*
31116657 TTTTATA
1 TTTAATA
31116664 TTTAATA
1 TTTAATA
31116671 TTTAATA
1 TTTAATA
31116678 ATTTTATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAATA
Found at i:31116666 original size:15 final size:15
Alignment explanation
Indices: 31116640--31116698 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
31116630 ATATTGTTTT
31116640 ATTTTAATATTTAATA
1 ATTTT-ATATTTAATA
31116656 ATTTTATATTTAAT-
1 ATTTTATATTTAATA
* *
31116670 ATTTAATAATTTTATA
1 ATTTTAT-ATTTAATA
*
31116686 CATTTTTTATTTA
1 -ATTTTATATTTA
31116699 TTGAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.17
15 15 0.43
16 9 0.26
17 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTATATTTAATA
Found at i:31116669 original size:22 final size:22
Alignment explanation
Indices: 31116636--31116685 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
31116626 AAATATATTG
31116636 TTTTAT-TTTAATATTTAATAA
1 TTTTATATTTAATATTTAATAA
31116657 TTTTATATTTAATATTTAATAA
1 TTTTATATTTAATATTTAATAA
31116679 TTTTATA
1 TTTTATA
31116686 CATTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTATATTTAATATTTAATAA
Found at i:31124481 original size:38 final size:38
Alignment explanation
Indices: 31124439--31124511 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
31124429 TATGAACCTA
31124439 TTGATATTTAATAATATAACTTAATAATTTGATCAAAT
1 TTGATATTTAATAATATAACTTAATAATTTGATCAAAT
31124477 TTGATATTTAATAATATAACTTAATAATTTGATCA
1 TTGATATTTAATAATATAACTTAATAATTTGATCA
31124512 GACTTAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Consensus pattern (38 bp):
TTGATATTTAATAATATAACTTAATAATTTGATCAAAT
Found at i:31127038 original size:45 final size:45
Alignment explanation
Indices: 31126974--31127059 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
31126964 ATGCTATATT
31126974 TATATTTATATTAGGGTTGATTATTAATGCCAAACTAATTTACTC
1 TATATTTATATTAGGGTTGATTATTAATGCCAAACTAATTTACTC
31127019 TATATTTATATTAGGGTTGATTATTAATGCCAAACTAATTT
1 TATATTTATATTAGGGTTGATTATTAATGCCAAACTAATTT
31127060 TTTTGTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (45 bp):
TATATTTATATTAGGGTTGATTATTAATGCCAAACTAATTTACTC
Found at i:31132130 original size:15 final size:15
Alignment explanation
Indices: 31132110--31132139 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31132100 AAAGGCAAAT
*
31132110 GAAATCCTTTGTTTG
1 GAAATCCATTGTTTG
31132125 GAAATCCATTGTTTG
1 GAAATCCATTGTTTG
31132140 CAGGCTCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (15 bp):
GAAATCCATTGTTTG
Found at i:31162302 original size:18 final size:18
Alignment explanation
Indices: 31162281--31162319 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31162271 CCTGTTTTAA
31162281 ATTTTGTTAGTTTTTT-TT
1 ATTTTGTTA-TTTTTTATT
*
31162299 ATTTTTTTATTTTTTATT
1 ATTTTGTTATTTTTTATT
31162317 ATT
1 ATT
31162320 AATTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
ATTTTGTTATTTTTTATT
Found at i:31163113 original size:71 final size:71
Alignment explanation
Indices: 31162997--31163141 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
31162987 GTTAAATTTC
31162997 ATAATACACTAGAAGTACCTAAGTAAGAATGTTTGATGATTCCATATGAGATATAAGTCTTTTAG
1 ATAATACACTAGAAGTACCTAAGTAAGAATGTTTGATGATTCCATATGAGATATAAGTCTTTTAG
31163062 ATAGTA
66 ATAGTA
31163068 ATAATACACTAGAAGTACCTAAGTAAGAATGTTTGATGATTCCATATGAGATATAAGTCTTTTAG
1 ATAATACACTAGAAGTACCTAAGTAAGAATGTTTGATGATTCCATATGAGATATAAGTCTTTTAG
31163133 ATAGTA
66 ATAGTA
31163139 ATA
1 ATA
31163142 TAGACATGAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (71 bp):
ATAATACACTAGAAGTACCTAAGTAAGAATGTTTGATGATTCCATATGAGATATAAGTCTTTTAG
ATAGTA
Found at i:31170177 original size:25 final size:25
Alignment explanation
Indices: 31170141--31170192 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
31170131 TAGGCTCAAG
*
31170141 GCTTGATAATATACACTGACACAAA
1 GCTTGATAATATACACCGACACAAA
*
31170166 GCTTGATTATATACACCGACACAAA
1 GCTTGATAATATACACCGACACAAA
31170191 GC
1 GC
31170193 CTACTAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (25 bp):
GCTTGATAATATACACCGACACAAA
Found at i:31174098 original size:18 final size:18
Alignment explanation
Indices: 31174060--31174095 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31174050 CCCATATTAC
*
31174060 ATATATATTTGATATATA
1 ATATATATTTGATATAAA
31174078 ATATATATTTGAT-TAAA
1 ATATATATTTGATATAAA
31174095 A
1 A
31174096 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
ATATATATTTGATATAAA
Found at i:31181991 original size:18 final size:19
Alignment explanation
Indices: 31181968--31182004 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
31181958 CATGAAATTC
31181968 ACATAA-TTATATT-TGATA
1 ACATAACTTA-ATTATGATA
31181986 ACATAACTTAATTATGATA
1 ACATAACTTAATTATGATA
31182005 TAAATACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (19 bp):
ACATAACTTAATTATGATA
Found at i:31182560 original size:2 final size:2
Alignment explanation
Indices: 31182555--31182584 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31182545 CATCCATCTC
*
31182555 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31182585 CCATTACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:31182969 original size:226 final size:227
Alignment explanation
Indices: 31182564--31183017 Score: 901
Period size: 226 Copynumber: 2.0 Consensus size: 227
31182554 CATATATATA
31182564 TATATATATATATTTATATATCCATTACACATTCTTCTCATTTGAATTCACATAGTTAAGAGATA
1 TATATATATATATTTATATATCCATTACACATTCTTCTCATTTGAATTCACATAGTTAAGAGATA
31182629 ATAAGTAAACATAACATCTATGAAACATTGCATATATTAAGAAATGGATTCCATGCATATTTCAT
66 ATAAGTAAACATAACATCTATGAAACATTGCATATATTAAGAAATGGATTCCATGCATATTTCAT
31182694 CCATCACATGATAAATATTCACACTTTTCATTTTATATATGCATATCAATTTTTTTCATTTCATG
131 CCATCACATGATAAATATTCACACTTTTCATTTTATATATGCATATCAATTTTTTTCATTTCATG
31182759 TGAACATTAGTAACATTAAGCCTTTATACATG
196 TGAACATTAGTAACATTAAGCCTTTATACATG
31182791 TATATATATA-ATTTATATATCCATTACACATTCTTCTCATTTGAATTCACATAGTTAAGAGATA
1 TATATATATATATTTATATATCCATTACACATTCTTCTCATTTGAATTCACATAGTTAAGAGATA
31182855 ATAAGTAAACATAACATCTATGAAACATTGCATATATTAAGAAATGGATTCCATGCATATTTCAT
66 ATAAGTAAACATAACATCTATGAAACATTGCATATATTAAGAAATGGATTCCATGCATATTTCAT
31182920 CCATCACATGATAAATATTCACACTTTTCATTTTATATATGCATATCAATTTTTTTCATTTCATG
131 CCATCACATGATAAATATTCACACTTTTCATTTTATATATGCATATCAATTTTTTTCATTTCATG
31182985 TGAACATTAGTAACATTAAGCCTTTATACATG
196 TGAACATTAGTAACATTAAGCCTTTATACATG
31183017 T
1 T
31183018 CTATCCATGA
Statistics
Matches: 227, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
226 217 0.96
227 10 0.04
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (227 bp):
TATATATATATATTTATATATCCATTACACATTCTTCTCATTTGAATTCACATAGTTAAGAGATA
ATAAGTAAACATAACATCTATGAAACATTGCATATATTAAGAAATGGATTCCATGCATATTTCAT
CCATCACATGATAAATATTCACACTTTTCATTTTATATATGCATATCAATTTTTTTCATTTCATG
TGAACATTAGTAACATTAAGCCTTTATACATG
Found at i:31183399 original size:25 final size:25
Alignment explanation
Indices: 31183363--31183420 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
31183353 TGATAGGCAT
*
31183363 AAAGCCTAATTATATACACCAGAAC
1 AAAGCCTGATTATATACACCAGAAC
* * *
31183388 AAAGCCTGATTATATATACTAGCAC
1 AAAGCCTGATTATATACACCAGAAC
31183413 AAAGCCTG
1 AAAGCCTG
31183421 CTAGGCACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.22
Consensus pattern (25 bp):
AAAGCCTGATTATATACACCAGAAC
Found at i:31185032 original size:17 final size:16
Alignment explanation
Indices: 31185010--31185044 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
31185000 ACATTGAGAA
31185010 TAATTTTAGTAAGTTTT
1 TAATTTTAGTAA-TTTT
*
31185027 TAATTTTATTAATTTT
1 TAATTTTAGTAATTTT
31185043 TA
1 TA
31185045 GAGTTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
TAATTTTAGTAATTTT
Found at i:31189121 original size:43 final size:43
Alignment explanation
Indices: 31189069--31189320 Score: 316
Period size: 43 Copynumber: 6.0 Consensus size: 43
31189059 GCGGCATTTT
* * * *
31189069 TAGCGGCGTTTGTGGGAAAAGCGCTGTTAAAAGTCATGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
* * **
31189112 TAGTGGCGTTTATGGGAAAAGCGTTGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
*
31189155 TAGCGGC-ATT-T--GAAAAGCGCCGCTAAAGG-CTGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-GTGGTCTA
* * * *
31189194 TAGCGGCGTTTGTGGGAAAAACACCGCTAAAGGTCGTGGTTTG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
*
31189237 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
* *
31189280 TAGCGACGTTTGTGGGAAAAGTGCCGCTAAAGGTCGTGGTC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTC
31189321 AGTATATTTG
Statistics
Matches: 180, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
38 1 0.01
39 31 0.17
40 2 0.01
41 2 0.01
42 2 0.01
43 141 0.78
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
Found at i:31193254 original size:27 final size:27
Alignment explanation
Indices: 31192951--31193317 Score: 352
Period size: 27 Copynumber: 13.6 Consensus size: 27
31192941 AATGGGCCTC
* *
31192951 TAAAATAACTGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* *
31192978 TAAAATTACCGAAACACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
*
31193005 TAAAATTACCGAAATACCAC-CGATGGG
1 TAAAATGACCGAAATACC-CTCGATGGG
* * * * *
31193032 TAAAATAATCAAAATACCCTCAATAGG
1 TAAAATGACCGAAATACCCTCGATGGG
31193059 TAAAATGACCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* ** *
31193086 TAAAATTATTGAAATACCCTTGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* *
31193113 TAAAATTACCGAAATACCCTCGATGAG
1 TAAAATGACCGAAATACCCTCGATGGG
* **
31193140 TAAAATGACTGAAATACCCTTAATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
* * * * *
31193167 TGAAATTATCAAAATACCCTCAATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
*
31193194 TAAAATGATCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGATGGG
**
31193221 TAAAATGATTGAAATACCCTCG-TAGGG
1 TAAAATGACCGAAATACCCTCGAT-GGG
* *
31193248 TAAAATGACTGTAATACCC-CTG-TAGGG
1 TAAAATGACCGAAATACCCTC-GAT-GGG
31193275 TAAAATGACC-ATAATA-CCTC-ATAGGG
1 TAAAATGACCGA-AATACCCTCGAT-GGG
* *
31193301 TTAAATGACCAAAATAC
1 TAAAATGACCGAAATAC
31193318 TCATGTAAGG
Statistics
Matches: 288, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.08
27 264 0.92
28 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGATGGG
Found at i:31193306 original size:26 final size:26
Alignment explanation
Indices: 31193191--31193362 Score: 93
Period size: 27 Copynumber: 6.5 Consensus size: 26
31193181 TACCCTCAAT
*
31193191 GGGTAAAATGATCGA-AATACCCTCGAT-
1 GGGTAAAATGA-CCATAATA-CCTC-ATA
** *
31193218 GGGTAAAATGATTGA-AATACCCTCGTA
1 GGGTAAAATGA-CCATAATA-CCTCATA
** * *
31193245 GGGTAAAATGACTGTAATACCCCTGTA
1 GGGTAAAATGACCATAATACCTC-ATA
31193272 GGGTAAAATGACCATAATACCTCATA
1 GGGTAAAATGACCATAATACCTCATA
* *
31193298 GGGTTAAATGACCAAAATA-CTCATGTA
1 GGGTAAAATGACCATAATACCTCA--TA
* * * * *
31193325 AGGTAAAATGATCGTAATGCCTCTAGA
1 GGGTAAAATGACCATAATACCTC-ATA
31193352 GGGT-AAATGAC
1 GGGTAAAATGAC
31193363 TATTTTGACC
Statistics
Matches: 117, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.03
26 29 0.25
27 80 0.68
28 3 0.03
29 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (26 bp):
GGGTAAAATGACCATAATACCTCATA
Found at i:31193416 original size:24 final size:24
Alignment explanation
Indices: 31193384--31193441 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
31193374 TCGAGTGTAA
* *
31193384 ATGATTGATTTGTCTGTGATTGGT
1 ATGACTGATTTGTCCGTGATTGGT
*
31193408 ATGACTGATTTGTCCGTGATTTGT
1 ATGACTGATTTGTCCGTGATTGGT
31193432 ATGACTGATT
1 ATGACTGATT
31193442 CTAAGCATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.47
Consensus pattern (24 bp):
ATGACTGATTTGTCCGTGATTGGT
Found at i:31193566 original size:27 final size:27
Alignment explanation
Indices: 31193510--31193566 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
31193500 GGAAGTACTG
*
31193510 TACTGGTGGCTCTGCCACAATCACTGT
1 TACTGGTGGCTCTGCCACAATCACTAT
31193537 TACTGGTGGCT-TGGCCACATAT-ACTAT
1 TACTGGTGGCTCT-GCCACA-ATCACTAT
31193564 TAC
1 TAC
31193567 ATGTAGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 1 0.04
27 24 0.89
28 2 0.07
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACAATCACTAT
Found at i:31193657 original size:32 final size:32
Alignment explanation
Indices: 31193613--31193737 Score: 142
Period size: 32 Copynumber: 3.9 Consensus size: 32
31193603 GTTTCGATGC
** *
31193613 TACTGATGGCTTTGTGTTGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* *
31193645 TACTGATAGCTTTGGGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* * ***
31193677 TACTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCAT
* *
31193709 TACTGATGGGTTTGTGCCAATCATATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
31193738 TGTACTTATG
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCAT
Found at i:31193699 original size:64 final size:64
Alignment explanation
Indices: 31193613--31193737 Score: 160
Period size: 64 Copynumber: 2.0 Consensus size: 64
31193603 GTTTCGATGC
* ** * * *
31193613 TACTGATGGCTTTGTGTTGATCATATTACCGTTACTGATAGCTTTGGGCCGATCATATTACCAT
1 TACTGATGGCTGTGTGCCGATCATATCACCGCTACTGATAGCTTTGGGCCAATCATATTACCAT
* * * *
31193677 TACTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGGTTTGTGCCAATCATATTAC
1 TACTGATGGCTGTGTGCCGATCATATCACCGCTACTGATAGCTTTGGGCCAATCATATTAC
31193738 TGTACTTATG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (64 bp):
TACTGATGGCTGTGTGCCGATCATATCACCGCTACTGATAGCTTTGGGCCAATCATATTACCAT
Found at i:31195660 original size:24 final size:24
Alignment explanation
Indices: 31195628--31195676 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
31195618 GAAGTTCAAC
31195628 AATTGAAAAAAATTCTCAATCTAA
1 AATTGAAAAAAATTCTCAATCTAA
*
31195652 AATTGAAAAAAATTCTCGATCTAA
1 AATTGAAAAAAATTCTCAATCTAA
31195676 A
1 A
31195677 CCAACTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (24 bp):
AATTGAAAAAAATTCTCAATCTAA
Found at i:31203695 original size:211 final size:211
Alignment explanation
Indices: 31203331--31203754 Score: 794
Period size: 211 Copynumber: 2.0 Consensus size: 211
31203321 CACTCACAGG
*
31203331 TTGAGAAGAAAATTGTTCAAGAGCTTGTTGATTATTGTTAGTCTAGATTCAACACCCTCACTATT
1 TTGAGAAGAAAATTGTTCAAGAGCTTGTTGATTATTGTTAGTCTAGATTCAACACCCTCACTATG
31203396 TCTAGCCTTAAAGGGAAATGTATTTTCGTGAAACATGGCATCTAAGGATTCAATTATAACATTGT
66 TCTAGCCTTAAAGGGAAATGTATTTTCGTGAAACATGGCATCTAAGGATTCAATTATAACATTGT
* *
31203461 TATCAAGGTTGAGCAACTTGTATGCGTTACTTATCAAGGCATAACCCATAAATGCATATCTAGAG
131 TATCAAGGTTGAGAAACTTGTATGCGTTACTCATCAAGGCATAACCCATAAATGCATATCTAGAG
31203526 GCTTTTACCCCAAGTT
196 GCTTTTACCCCAAGTT
*
31203542 TTGAGAAGAAAATTGTTCAAGGGCTTGTTGATTATTGTTAGTCTAGATTCAACACCCTCACTATG
1 TTGAGAAGAAAATTGTTCAAGAGCTTGTTGATTATTGTTAGTCTAGATTCAACACCCTCACTATG
* *
31203607 TCTAGCCTTAAAGGGAAATGTATTTTTGTGAAGCATGGCATCTAAGGATTCAATTATAACATTGT
66 TCTAGCCTTAAAGGGAAATGTATTTTCGTGAAACATGGCATCTAAGGATTCAATTATAACATTGT
31203672 TATCAAGGTTGAGAAACTTGTATGCGTTACTCATCAAGGCATAACCCATAAATGCATATCTAGAG
131 TATCAAGGTTGAGAAACTTGTATGCGTTACTCATCAAGGCATAACCCATAAATGCATATCTAGAG
31203737 GCTTTTACCCCAAGTT
196 GCTTTTACCCCAAGTT
31203753 TT
1 TT
31203755 AGACTTTTAT
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
211 207 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (211 bp):
TTGAGAAGAAAATTGTTCAAGAGCTTGTTGATTATTGTTAGTCTAGATTCAACACCCTCACTATG
TCTAGCCTTAAAGGGAAATGTATTTTCGTGAAACATGGCATCTAAGGATTCAATTATAACATTGT
TATCAAGGTTGAGAAACTTGTATGCGTTACTCATCAAGGCATAACCCATAAATGCATATCTAGAG
GCTTTTACCCCAAGTT
Found at i:31212653 original size:41 final size:41
Alignment explanation
Indices: 31212596--31212683 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
31212586 NNNNNNNNNN
31212596 TGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCC
1 TGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCC
*
31212637 TGCTAGGTTTATAACCTGATTCAGATTACCGGCACTTAGCC
1 TGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCC
31212678 TGCTAG
1 TGCTAG
31212684 ACGTATAGTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (41 bp):
TGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCC
Found at i:31218025 original size:21 final size:21
Alignment explanation
Indices: 31217999--31218057 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
31217989 GACCTTGTTA
31217999 ACAAATTTGTTCATTTTTTAC
1 ACAAATTTGTTCATTTTTTAC
* **
31218020 ACAAATTTATTCATTTTTTTGT
1 ACAAATTTGTTCA-TTTTTTAC
31218042 ACAAATTTTGTTCATT
1 ACAAA-TTTGTTCATT
31218058 CATTTGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 12 0.38
22 13 0.41
23 7 0.22
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (21 bp):
ACAAATTTGTTCATTTTTTAC
Found at i:31218049 original size:22 final size:21
Alignment explanation
Indices: 31217999--31218038 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31217989 GACCTTGTTA
*
31217999 ACAAATTTGTTCATTTTTTAC
1 ACAAATTTATTCATTTTTTAC
31218020 ACAAATTTATTCATTTTTT
1 ACAAATTTATTCATTTTTT
31218039 TGTACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (21 bp):
ACAAATTTATTCATTTTTTAC
Found at i:31218065 original size:23 final size:20
Alignment explanation
Indices: 31217999--31218057 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
31217989 GACCTTGTTA
31217999 ACAAATTTGTTCATTTTT-T
1 ACAAATTTGTTCATTTTTGT
*
31218018 ACACAAATTTATTCATTTTTTTGT
1 --ACAAATTTGTTCA--TTTTTGT
31218042 ACAAATTTTGTTCATT
1 ACAAA-TTTGTTCATT
31218058 CATTTGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 14 0.44
22 5 0.16
23 12 0.38
24 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (20 bp):
ACAAATTTGTTCATTTTTGT
Found at i:31224583 original size:2 final size:2
Alignment explanation
Indices: 31224578--31224602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31224568 AAATGAGATT
31224578 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31224603 GTTTCGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31241400 original size:28 final size:28
Alignment explanation
Indices: 31241340--31241402 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
31241330 TATTTTTCAT
*
31241340 TTTGGTTTGTATCGTTTCTATGCAATAA
1 TTTGTTTTGTATCGTTTCTATGCAATAA
*
31241368 TTTGTTTTGTATCGTTTCTGTGCAATAA
1 TTTGTTTTGTATCGTTTCTATGCAATAA
31241396 TTTGTTT
1 TTTGTTT
31241403 ACTCTTAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.56
Consensus pattern (28 bp):
TTTGTTTTGTATCGTTTCTATGCAATAA
Found at i:31246006 original size:105 final size:105
Alignment explanation
Indices: 31245794--31245981 Score: 245
Period size: 105 Copynumber: 1.8 Consensus size: 105
31245784 GTTTTTTTTC
** *
31245794 TTAAAAATGTATTGGCCCTTTTGACGCAAAGAGGGAAGACTGCCCAAGCACCTCACCCAGGTTAC
1 TTAAAAATGTATTGGCCCTTTTGACGCAAAGAGGGAAGACAACCCAAGCACCCCACCCAGGTTAC
* * **
31245859 TCAGCCCAACACATTCTTATTTTATTATATATATTTGTGG
66 TCAGCCCAACACACTCTTATTTTATTATATATAATTCCGG
* * * *
31245899 TTAAGAATGTTTTGGCCCTTTTGACGCGAAA-AGGGATGACAACCCAAGCACCCCACCCCGGTTA
1 TTAAAAATGTATTGGCCCTTTTGACGC-AAAGAGGGAAGACAACCCAAGCACCCCACCCAGGTTA
*
31245963 CTC-TCCCAACACACTCTTA
65 CTCAGCCCAACACACTCTTA
31245982 AGTTTTTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
104 14 0.19
105 56 0.77
106 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (105 bp):
TTAAAAATGTATTGGCCCTTTTGACGCAAAGAGGGAAGACAACCCAAGCACCCCACCCAGGTTAC
TCAGCCCAACACACTCTTATTTTATTATATATAATTCCGG
Found at i:31246016 original size:105 final size:105
Alignment explanation
Indices: 31245805--31246016 Score: 234
Period size: 105 Copynumber: 2.0 Consensus size: 105
31245795 TAAAAATGTA
** *
31245805 TTGGCCCTTTTGACGCAAAGAGGGAAGACTGCCCAAGCACCTCACCCAGGTTACTCAGCCCAACA
1 TTGGCCCTTTTGACGCAAAGAGGGAAGACAACCCAAGCACCCCACCCAGGTTACTCAGCCCAACA
* * ** *
31245870 CATTCTTATTTTATTATATATATTTGTGGTTAAGAATGTT
66 CACTCTTATTTTATTATATATAATTCCGGTTAAGAAAGTT
* * *
31245910 TTGGCCCTTTTGACGCGAAA-AGGGATGACAACCCAAGCACCCCACCCCGGTTACTC-TCCCAAC
1 TTGGCCCTTTTGACGC-AAAGAGGGAAGACAACCCAAGCACCCCACCCAGGTTACTCAGCCCAAC
* * *
31245973 ACACTCTTAAGTTTT-TTTTCTTTAATTCCGGTT-AGAAGAGTT
65 ACACTCTT-A-TTTTATTATATATAATTCCGGTTAAGAA-AGTT
31246015 TT
1 TT
31246017 ATGTAACATG
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
104 17 0.19
105 65 0.73
106 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (105 bp):
TTGGCCCTTTTGACGCAAAGAGGGAAGACAACCCAAGCACCCCACCCAGGTTACTCAGCCCAACA
CACTCTTATTTTATTATATATAATTCCGGTTAAGAAAGTT
Found at i:31250526 original size:12 final size:12
Alignment explanation
Indices: 31250509--31250539 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31250499 AAATAATATC
31250509 ATAATAATCCTA
1 ATAATAATCCTA
31250521 ATAATAATCCTA
1 ATAATAATCCTA
*
31250533 AAAATAA
1 ATAATAA
31250540 AATTTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATAATCCTA
Found at i:31256801 original size:46 final size:46
Alignment explanation
Indices: 31256720--31256880 Score: 229
Period size: 46 Copynumber: 3.6 Consensus size: 46
31256710 TTTGAGTACT
* *
31256720 TCTGATCAAGTGACAAAGTGATAAATGATAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
* * *
31256766 TCTCATCAAGTGACAAAGTGATAGGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
* *
31256812 TCTGATCAAGTGACAAAGTGATAAGTGATAGC-CTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
*
31256857 TCTGATC-AGGGAC-AAGTGATAAGT
1 TCTGATCAAGTGACAAAGTGATAAGT
31256881 AATCATACAT
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
43 11 0.11
44 5 0.05
45 18 0.17
46 70 0.67
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
Found at i:31258292 original size:21 final size:23
Alignment explanation
Indices: 31258258--31258299 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
31258248 GATATAGCTA
31258258 TAAAATGAACAAAT-GGTGAAGT
1 TAAAATGAACAAATGGGTGAAGT
*
31258280 TAAAA-GATCAAATGGGTGAA
1 TAAAATGAACAAATGGGTGAA
31258300 AAATAAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (23 bp):
TAAAATGAACAAATGGGTGAAGT
Found at i:31261964 original size:46 final size:46
Alignment explanation
Indices: 31261914--31262174 Score: 416
Period size: 46 Copynumber: 5.7 Consensus size: 46
31261904 TTTGAGTACT
*
31261914 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
31261960 TCTGATCAAGTGACAAAGTGATAAGTAGTAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
31262006 TCTCATCAAGTGACAGAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
31262052 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * * * *
31262098 TTTGATCAAGTGAAAAAGTGATAAGTGATAG-TCTAGCTACAGTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
31262143 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC
31262175 NNNNNNNNNN
Statistics
Matches: 195, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 40 0.21
46 155 0.79
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:31271020 original size:9 final size:9
Alignment explanation
Indices: 31271006--31271031 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31270996 AACACCAAGC
31271006 CAGTCTTAA
1 CAGTCTTAA
31271015 CAGTCTTAA
1 CAGTCTTAA
31271024 CAGTCTTA
1 CAGTCTTA
31271032 GCATCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (9 bp):
CAGTCTTAA
Found at i:31280887 original size:13 final size:13
Alignment explanation
Indices: 31280869--31280894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31280859 CAGTGAGCAG
31280869 ATTCTGATAAAAT
1 ATTCTGATAAAAT
31280882 ATTCTGATAAAAT
1 ATTCTGATAAAAT
31280895 GTTATGCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTCTGATAAAAT
Found at i:31281819 original size:18 final size:17
Alignment explanation
Indices: 31281793--31281828 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31281783 TTTGGTTATA
31281793 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
31281811 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
31281828 T
1 T
31281829 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Done.